The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus

The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1α gene in the formation of this protease. The effects of tRNA abundance of the pigs...

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Main Authors:	Yao-zhong Ding, Ya-nan You, Dong-jie Sun, Hao-tai Chen, Yong-lu Wang, Hui-yun Chang, Li Pan, Yu-zhen Fang, Zhong-wang Zhang, Peng Zhou, Jian-liang Lv, Xin-sheng Liu, Jun-jun Shao, Fu-rong Zhao, Tong Lin, Laszlo Stipkovits, Zygmunt Pejsak, Yong-guang Zhang, Jie Zhang
Format:	Article
Language:	English
Published:	Hindawi Limited 2014-01-01
Series:	BioMed Research International
Online Access:	http://dx.doi.org/10.1155/2014/765320

id	doaj-dbd8f100ed2543718456729224edc40f
record_format	Article
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Yao-zhong Ding Ya-nan You Dong-jie Sun Hao-tai Chen Yong-lu Wang Hui-yun Chang Li Pan Yu-zhen Fang Zhong-wang Zhang Peng Zhou Jian-liang Lv Xin-sheng Liu Jun-jun Shao Fu-rong Zhao Tong Lin Laszlo Stipkovits Zygmunt Pejsak Yong-guang Zhang Jie Zhang
spellingShingle	Yao-zhong Ding Ya-nan You Dong-jie Sun Hao-tai Chen Yong-lu Wang Hui-yun Chang Li Pan Yu-zhen Fang Zhong-wang Zhang Peng Zhou Jian-liang Lv Xin-sheng Liu Jun-jun Shao Fu-rong Zhao Tong Lin Laszlo Stipkovits Zygmunt Pejsak Yong-guang Zhang Jie Zhang The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus BioMed Research International
author_facet	Yao-zhong Ding Ya-nan You Dong-jie Sun Hao-tai Chen Yong-lu Wang Hui-yun Chang Li Pan Yu-zhen Fang Zhong-wang Zhang Peng Zhou Jian-liang Lv Xin-sheng Liu Jun-jun Shao Fu-rong Zhao Tong Lin Laszlo Stipkovits Zygmunt Pejsak Yong-guang Zhang Jie Zhang
author_sort	Yao-zhong Ding
title	The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus
title_short	The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus
title_full	The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus
title_fullStr	The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus
title_full_unstemmed	The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus
title_sort	effects of the context-dependent codon usage bias on the structure of the nsp1α of porcine reproductive and respiratory syndrome virus
publisher	Hindawi Limited
series	BioMed Research International
issn	2314-6133 2314-6141
publishDate	2014-01-01
description	The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1α gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1α on shaping the specific folding units (α-helix, β-strand, and the coil) in the nsp1α were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1α of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1α, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1α, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1α. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1α was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1α. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1α structure.
url	http://dx.doi.org/10.1155/2014/765320
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spelling	doaj-dbd8f100ed2543718456729224edc40f2020-11-24T22:46:09ZengHindawi LimitedBioMed Research International2314-61332314-61412014-01-01201410.1155/2014/765320765320The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome VirusYao-zhong Ding0Ya-nan You1Dong-jie Sun2Hao-tai Chen3Yong-lu Wang4Hui-yun Chang5Li Pan6Yu-zhen Fang7Zhong-wang Zhang8Peng Zhou9Jian-liang Lv10Xin-sheng Liu11Jun-jun Shao12Fu-rong Zhao13Tong Lin14Laszlo Stipkovits15Zygmunt Pejsak16Yong-guang Zhang17Jie Zhang18State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaRT-Europe Research Center Ltd., Budapest, HungaryDepartment of Swine Diseases, National Veterinary Research Institute, 57 Partyzantow, 24-100 Puławy, PolandState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaState Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, ChinaThe information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1α gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1α on shaping the specific folding units (α-helix, β-strand, and the coil) in the nsp1α were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1α of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1α, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1α, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1α. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1α was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1α. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1α structure.http://dx.doi.org/10.1155/2014/765320

The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus

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